rs2252824

Variant names:

• chr20-23374111-G-A
• rs2252824

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.249 in 152,052 control chromosomes in the GnomAD database, including 5,416 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37880 AN: 151934 Hom.: 5417 Cov.: 32

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.267

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.249 AC: 37877 AN: 152052 Hom.: 5416 Cov.: 32 AF XY: 0.253 AC XY: 18804 AN XY: 74288

Gnomad4 AFR AF: 0.0936

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.266

Alfa AF: 0.282 Hom.: 1061

Bravo AF: 0.247

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2252824; hg19: chr20-23354748;